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LncRNAs expression signatures of renal clear cell carcinoma revealed by microarray.

Yu G, Yao W, Wang J, Ma X, Xiao W, Li H, Xia D, Yang Y, Deng K, Xiao H, Wang B, Guo X, Guan W, Hu Z, Bai Y, Xu H, Liu J, Zhang X, Ye Z - PLoS ONE (2012)

Bottom Line: From the data we found there were thousands of lncRNAs that differentially expressed (≥ 2 fold-change) in RCCC tissues compared with NT and 916 lncRNAs differentially expressed in five or more of six RCCC samples.The four lncRNAs were aberrantly expressed in RCCC compared with matched histologically normal renal tissues.The results displayed that clusters of lncRNAs were aberrantly expressed in RCCC compared with NT samples, which revealed that lncRNAs differentially expressed in tumor tissues and normal tissues may exert a partial or key role in tumor development.

View Article: PubMed Central - PubMed

Affiliation: Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.

ABSTRACT

Background: Long noncoding RNAs (lncRNAs) are an important class of pervasive genes involved in a variety of biological functions. They are aberrantly expressed in many types of cancers. In this study, we described lncRNAs profiles in 6 pairs of human renal clear cell carcinoma (RCCC) and the corresponding adjacent nontumorous tissues (NT) by microarray.

Methodology/principal findings: With abundant and varied probes accounting 33,045 LncRNAs in our microarray, the number of lncRNAs that expressed at a certain level could be detected is 17157. From the data we found there were thousands of lncRNAs that differentially expressed (≥ 2 fold-change) in RCCC tissues compared with NT and 916 lncRNAs differentially expressed in five or more of six RCCC samples. Compared with NT, many lncRNAs were significantly up-regulated or down-regulated in RCCC. Our data showed that down-regulated lncRNAs were more common than up-regulated ones. ENST00000456816, X91348, BC029135, NR_024418 were evaluated by qPCR in sixty-three pairs of RCCC and NT samples. The four lncRNAs were aberrantly expressed in RCCC compared with matched histologically normal renal tissues.

Conclusions/significance: Our study is the first one to determine genome-wide lncRNAs expression patterns in RCCC by microarray. The results displayed that clusters of lncRNAs were aberrantly expressed in RCCC compared with NT samples, which revealed that lncRNAs differentially expressed in tumor tissues and normal tissues may exert a partial or key role in tumor development. Taken together, this study may provide potential targets for future treatment of RCCC and novel insights into cancer biology.

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Related in: MedlinePlus

Counts of up-regulated and down-regulated lncRNAs.Many lncRNAs were determined to be significantly up-regulated or down-regulated in RCCC samples compared with NT samples in six patients by microarray. The counts of up-regulated and down-regulated lncRNAs varied across the six patients. In four out of six RCCC patients down-regulated lncRNAs were more common than up-regulated ones. Two patient down-regulated lncRNAs were less common than up-regulated ones.
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pone-0042377-g001: Counts of up-regulated and down-regulated lncRNAs.Many lncRNAs were determined to be significantly up-regulated or down-regulated in RCCC samples compared with NT samples in six patients by microarray. The counts of up-regulated and down-regulated lncRNAs varied across the six patients. In four out of six RCCC patients down-regulated lncRNAs were more common than up-regulated ones. Two patient down-regulated lncRNAs were less common than up-regulated ones.

Mentions: Next, from the microarray data we compared the lncRNAs expression levels between the six RCCC tissues and their matched normal tissues, and identified an average of 3837 long lncRNAs (range from 2262–5532) that were significantly differentially expressed (≥2-fold) (Table S1). The basic information of the six patients was shown in Table S2. The sequence obtaining procedure may vary depending upon the source of the lncRNA. The results demonstrated that tens of thousands lncRNAs could be examined in normal and tumor tissues, but only thousands of lncRNAs were significantly up-regulated or down-regulated, which could be used to discriminate RCCC from matched normal tissues (Table S1, Table S3). Compared with the NT tissues, a total of 3055 lncRNAs were found to be consistently up-regulated or down-regulated shared by 4 of the 6 RCCC samples and 1866 by 5 and 626 in all (Table S4). ENST00000429695 (Log2 Fold change T/N = −4.175355) was the most significantly down-regulated one while ENST00000456816 (Log2 Fold change T/N = 6.312544) was the most significantly up-regulated (Table 1). The number of up-regulated and down-regulated lncRNAs varied in different patients. We found that down-regulated lncRNAs were more common than up-regulated ones (Figure 1).


LncRNAs expression signatures of renal clear cell carcinoma revealed by microarray.

Yu G, Yao W, Wang J, Ma X, Xiao W, Li H, Xia D, Yang Y, Deng K, Xiao H, Wang B, Guo X, Guan W, Hu Z, Bai Y, Xu H, Liu J, Zhang X, Ye Z - PLoS ONE (2012)

Counts of up-regulated and down-regulated lncRNAs.Many lncRNAs were determined to be significantly up-regulated or down-regulated in RCCC samples compared with NT samples in six patients by microarray. The counts of up-regulated and down-regulated lncRNAs varied across the six patients. In four out of six RCCC patients down-regulated lncRNAs were more common than up-regulated ones. Two patient down-regulated lncRNAs were less common than up-regulated ones.
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC3412851&req=5

pone-0042377-g001: Counts of up-regulated and down-regulated lncRNAs.Many lncRNAs were determined to be significantly up-regulated or down-regulated in RCCC samples compared with NT samples in six patients by microarray. The counts of up-regulated and down-regulated lncRNAs varied across the six patients. In four out of six RCCC patients down-regulated lncRNAs were more common than up-regulated ones. Two patient down-regulated lncRNAs were less common than up-regulated ones.
Mentions: Next, from the microarray data we compared the lncRNAs expression levels between the six RCCC tissues and their matched normal tissues, and identified an average of 3837 long lncRNAs (range from 2262–5532) that were significantly differentially expressed (≥2-fold) (Table S1). The basic information of the six patients was shown in Table S2. The sequence obtaining procedure may vary depending upon the source of the lncRNA. The results demonstrated that tens of thousands lncRNAs could be examined in normal and tumor tissues, but only thousands of lncRNAs were significantly up-regulated or down-regulated, which could be used to discriminate RCCC from matched normal tissues (Table S1, Table S3). Compared with the NT tissues, a total of 3055 lncRNAs were found to be consistently up-regulated or down-regulated shared by 4 of the 6 RCCC samples and 1866 by 5 and 626 in all (Table S4). ENST00000429695 (Log2 Fold change T/N = −4.175355) was the most significantly down-regulated one while ENST00000456816 (Log2 Fold change T/N = 6.312544) was the most significantly up-regulated (Table 1). The number of up-regulated and down-regulated lncRNAs varied in different patients. We found that down-regulated lncRNAs were more common than up-regulated ones (Figure 1).

Bottom Line: From the data we found there were thousands of lncRNAs that differentially expressed (≥ 2 fold-change) in RCCC tissues compared with NT and 916 lncRNAs differentially expressed in five or more of six RCCC samples.The four lncRNAs were aberrantly expressed in RCCC compared with matched histologically normal renal tissues.The results displayed that clusters of lncRNAs were aberrantly expressed in RCCC compared with NT samples, which revealed that lncRNAs differentially expressed in tumor tissues and normal tissues may exert a partial or key role in tumor development.

View Article: PubMed Central - PubMed

Affiliation: Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.

ABSTRACT

Background: Long noncoding RNAs (lncRNAs) are an important class of pervasive genes involved in a variety of biological functions. They are aberrantly expressed in many types of cancers. In this study, we described lncRNAs profiles in 6 pairs of human renal clear cell carcinoma (RCCC) and the corresponding adjacent nontumorous tissues (NT) by microarray.

Methodology/principal findings: With abundant and varied probes accounting 33,045 LncRNAs in our microarray, the number of lncRNAs that expressed at a certain level could be detected is 17157. From the data we found there were thousands of lncRNAs that differentially expressed (≥ 2 fold-change) in RCCC tissues compared with NT and 916 lncRNAs differentially expressed in five or more of six RCCC samples. Compared with NT, many lncRNAs were significantly up-regulated or down-regulated in RCCC. Our data showed that down-regulated lncRNAs were more common than up-regulated ones. ENST00000456816, X91348, BC029135, NR_024418 were evaluated by qPCR in sixty-three pairs of RCCC and NT samples. The four lncRNAs were aberrantly expressed in RCCC compared with matched histologically normal renal tissues.

Conclusions/significance: Our study is the first one to determine genome-wide lncRNAs expression patterns in RCCC by microarray. The results displayed that clusters of lncRNAs were aberrantly expressed in RCCC compared with NT samples, which revealed that lncRNAs differentially expressed in tumor tissues and normal tissues may exert a partial or key role in tumor development. Taken together, this study may provide potential targets for future treatment of RCCC and novel insights into cancer biology.

Show MeSH
Related in: MedlinePlus